Information about software packages installed on the ICHEC systems.
VMD Visualisation Molecular Dynamics
VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
The VMD package is available for use by all ICHEC users.
To VMD use load the relevant environment module:
On Stokes, VMD is installed as a binary package. As it needs X11 display connection, the code is only available on the login nodes.
Further information can be obtained at www.ks.uiuc.edu/Research/vmd/.